RetrogeneDB ID: retro_opri_439

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_120342:911..1193(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOPRG00000007969
• Aliases: None
• Description: None

Sequence

>retro_opri_439
AATACAACCTCTCAATATTGGGGGAAAAAAGTGGCAGAAAAACAGAGGAATGCCTCTCGACAAAGGAAACACTCTTGACT
TAGGAAAAATGAGAAACTTCATAAAGAGATCAAACAAAAGGACATGAAATTGCCTGCTTGAAATAAGGAGAACAAAGAAT
TGGCAAAAGTAGTCAAATATATTCAGTGTACAACACAGGTAATACCGACACTGAATGACAGACCTCTGCATGACTTTGAA
TCACCTGATACTCAGGAATTTGATTCTGCAGGGGAAGCTGGC

Alignment

ORF - retro_opri_439 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.19 %
• Parental protein coverage: 75.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NAPSQYW-KEVAEKR----RKALYETLKENEKLHKEIEQRDNEIARLKKENKELAEVAEHVQYMAQVVET
          N..SQYW.K.VAEK.....R......L..NEKLHKEI.Q.D.......KENKELA.V....Q...QV..T
Retrocopy NTTSQYWGKKVAEKQRNASRQRKHS*LRKNEKLHKEIKQKDMKLPA*NKENKELAKVVKYIQCTTQVIPT

Parental  LSGVSLHDLESPDSQEFDSEEEAG
          L....LHD.ESPD.QEFDS..EAG
Retrocopy LNDRPLHDFESPDTQEFDSAGEAG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_439 was not experimentally validated.

Homology

Retrocopy orthology:

Ochotona princeps does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006161	1 retrocopy	retro_cjac_1012,
Microcebus murinus	ENSMICG00000014010	1 retrocopy	retro_mmur_594,
Myotis lucifugus	ENSMLUG00000014849	2 retrocopies	retro_mluc_1589, retro_mluc_743,
Monodelphis domestica	ENSMODG00000011682	1 retrocopy	retro_mdom_1800,
Mus musculus	ENSMUSG00000006715	2 retrocopies	retro_mmus_1525, retro_mmus_2213,
Oryctolagus cuniculus	ENSOCUG00000000728	1 retrocopy	retro_ocun_613,
Otolemur garnettii	ENSOGAG00000004982	1 retrocopy	retro_ogar_1726,
Ochotona princeps	ENSOPRG00000007969	1 retrocopy	retro_opri_439 ,
Rattus norvegicus	ENSRNOG00000018782	1 retrocopy	retro_rnor_820,
Sarcophilus harrisii	ENSSHAG00000004058	2 retrocopies	retro_shar_581, retro_shar_769,
Tupaia belangeri	ENSTBEG00000010502	2 retrocopies	retro_tbel_1028, retro_tbel_353,